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What are the Dreiding paramters for graphene ?
Closed | Responses: 1
I am using lammps to simulate PMMA-graphene composite system. I used polymer modeller to create the PMMA chains. I want to add the graphene sheet but I am not sure what...
when I runn with my own exe.lammps 3 minimize has done but at fix 1 all nvt temp 300.0 300.0 100.0 this error apear: ERROR: All pair coeffs are not set (../pair.cpp:175) I will be very thankfull.
how to get a final pdb structure
Why does my simulation end with an error?
I'm interested in building long polymer chains and was eager to try out this tool. However, it appears that I get an error when I begin a simulation of a polymer built from...
Polymer modeler and Mavericks
Closed | Responses: 2
Dear Sir, I'm trying to launch polymer modeler tool in a Mavericks MacOs machine and the site seems to be loading but nothing happens. My java version is updated (version 7 update 60). Can...
Is there a way to specify an orthogonal but non-cubic simulation box or is a cubic box the only option?
I can’t get LAMMPS output files
I’m trying to run a simulation of Nylon (PA6) using z-matrix. So it works when I try to get structure output only, but in case of LAMMPS output files it makes an error like that:
When I try to construct a single polymer chain either with the available monomers or with my own z-matrix, i get the following output in the log:
ERROR: builder failed:...
Can i get the simulation for catechol using nanohub?I did it for chitin and cellulose and got results cathechol is not a polymer.
Proper z-matrix format
I am finding it hard to make the z-matrix. I see that the z-matrices of all polymers within the tool starts with H as the initial atom. Open babel can give me the matrix...
Building certain polymers
I am using Polymer Builder for the first time. I am trying to build teo polymers. One of them is called PE-OC6http://nanohub.org/answers/question/1008
error when producing z-matrix
Open | Responses: 1
I tried to build 10 chains of Polyethylene, each contains 10 monomers. I wanted to produce only the z-matrix as the output. But it was failed. The error message I saw at the end was...
z-matrix of Polyacrylamide monomer
Dear The Polymer Modeler developers!
I build the z-matrix of Polyacrylamide monomer which is give below.
But in process of simulation of structure of polymer I get bad structure.
Maybe I was...
introduce a solvent
Diar The Polymer Modeler developers!
Can I introduce a solvent such as water or other in the simulation of polymers in Polymer Modeler?
I am trying to generate a polystyrene structure. Initially I was aiming for a single chain with 20 monomers. But once I loaded the lammps data file in vmd, I saw some bonds were missing....
error during equalization with polyethylene structure
I tried to model a polyethylene structure(50 monomers and 15 chains). I used mostly default settings. but while I am running the NVT equailization (I changed the timestep into 1...
save input data file
I would like to know whether I can save the polymer chain I made in polymer modeler.
limited number of polymer chains
Open | Responses: 4
Currently, I tried to build 100 PE chains with 10 monomers each. However, the PolymerModeler keeps...
“ERROR: Illegal fix nvt/npt/nph command”
I built a PE chain by using Polymer Modeler.
It seems working well, however, the follwing error occurs “ERROR: Illegal fix nvt/npt/nph command” when you run LAMMPS with the input...
How can I resolve the connection problem?
How can I resolved the connection problem? indeed I try to run in my nanoHUB.org the launch tools of polymer modeler but I am not directed to the polymer modeler’s...